How do I use Blender's built-in stereoscopic features?
It seems that the render result will always be either anaglyphic or both images overlaid. You can toggle it with one of the icons at the bottom.

Whatever stereoscopic format you choose when rendering doesn't seem to do any difference. It's when saving the result that you can choose the format. The same (or similar) panel is shown when choosing a name to save it as.
(This actually makes more sense since you may want to try out or save to different formats and it would be a shame if you had to render it again.)